Darkened Days
by Sezthekitty
Summary: The cloud that hung over Domino City had only grown over the years. No one was safe. Groups did not survive for long, but as Yugi and his friends were considered part of the rebellion their days were numbered even more. The enemy will stop at nothing, even bringing back the person Yugi longed so greatly to see again. Sadly the circumstances are anything but joyful. Mainly YY/AxY.


**A/N : This is actually the first Yu-Gi-Oh story that I have ever written. I'm not even sure if I want to continue this or not, but a while ago I uploaded this under the normal Yu-Gi-Oh category, but after much thought I deleted the original and am uploading this as a Cross-Over. Yu-Gi-Oh X Yu-Gi-Oh GX... Although I was firstly say that this story is mainly Yu-Gi-Oh, for the purpose of being under the category if this is continued to be written then I will involve GX characters more than I originally intended to. Either way this has been uploaded to the Cross Over because I think that GX members will play a big role in this story if it is continued, but as I am a huge fan of YGO the original Series you might find that the plot may come a little lacking of GX members at times. We'll just see if this goes anywhere.**

**The rating is only T because I become paranoid, but really I think it could be considered T+ it depends how dark this story ends up becoming.**

**Pairings - This will probably end up being a yaoi story if there are any pairings, I will possibly do a few straight pairings here and there, but it's only really if I do not feel that characters will end up with people I normally ship them with.**

**The most likely shippings for this story will turn out to be:**

**Puzzleshipping/Blindshipping and ****Puppyshipping**

**I will say that the Pharaoh's name is Atem but his nickname for Yugi is Yami - so I have selected Yami as the character tag.**

**I do not actually have an OTP for GX, so if this story is to continue to the point of GX pairings I will end up having a vote most likely to see who can go with who.**

**Apologies if some characters come off a little OC, I have not rewritten this story from when I first wrote it, because honestly I think it is pretty decently written so a rewrite will not be needed unless I am informed that there is something too confusing or wrong happening in this chapter.**

**I do not own any rights to either Yu-Gi-Oh or Yu-Gi-Oh GX, I make no profit from this. This is kinda being uploaded to see if there is any interest in continuing to write this, I remember I found great joy when I first wrote this, but because of the category confusions I do not think it was posted in the correct place and ended up simply forgetting about it.**

**Now, on to the start.**

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Dark sky clouded round the city of Domino, these were dark times. No one was safe, on this certain night, it would just make things even more confusing. As the tears of heaven beat down on to the the grey city, a voice could be heard, it was one word, no a name, that was screamed to the heavens, only covered by a bright flash of lightning.

"Syrus!"

A boy slowly fell to his knees, a torn cloak laying discarded beside him, a duel disk clinging to his arm, a half played game by his cards. Near the boy lead another unmoving, cards lay discarded around him as the rain beat down on to his pale skin.

Another flash of lightning, followed by a spine tingling cackle. A duel disk upon the cacklers arm, a half played game in the cards. Lightning hit the ground by them, forming something, it was coming more often now, only in this area.

The biggest lightning yet slammed it's way towards the ground, in the process, making something, something that should of never been made. A portal.

They were too late, this is what they were dueling to stop, but during that duel it had opened, the gateway to another world. If that world was what they thought it was, they'd all be doomed.

Soon enough the boy on his knees couldn't take it any more, he fell forward in to the world of unwanted sleep and darkness.

They had tried their best, but not everything can be predicted - this certainly wasn't something that was.

He cracked open his eyes weakly, he couldn't help but groan, he really didn't understand what this was. He felt wetness on his cheeks, no, all around him and on him. That wetness was cold, a word popped in to his head as he shut his eyes, after only being able to see blurs, 'rain'.

His eyes shot open again, blinking a few times. Where was this? wasn't he meant to be in the after life, in the spirit world, after all, he did loose the duel, he knew that for a fact. He also knew that when you loose the duel, he would be set free, but why was he here, in the world of the living.

No scratch that, why was he here in his own body with no puzzle. This wasn't making sense, he looked around him, he saw his after life friends - better known as his Egyptian friends, the ones that stayed by his side and welcomed him as he joined the light of the spirit world.

He turned his head in another direction, he saw two boys, one with blue hair, he looked weak a frail in his opinion, but he had long ago learned that appearances weren't everything. The other boy - no wait, was that even a boy, it looked like a Kuriboh, was it stuck on some ones head?

After a long few minutes, he started to see that the boy was moving again, trying to get up, that's when he decided that it was a boy, who just happened to look like he had a Kuriboh stuck to his head. Either way, it didn't matter, he was greatly confused about what was going on here.

He noticed a shadow moving over towards the two boys, it seem that he hadn't been noticed yet, or he had and was just ignoring them.

His eyes stuck to the boy with the Kuriboh hair like a hawk, as he pushed him self to his feet, even though he seemed to be strong, he could see the boy shaking like a leaf. The person belonging to the shadow soon grabbed the boy and held up a fist to punch him. Beating a man - no boy - when he could barely stand, it just proved who was good and who was not.

The blue haired boy also started to try and stand up, he was in a lot worst shape than Kuriboh boy, but it could of just been the fact that he looked more frail and overall weak than the other.

Before the man could contact his fist with the Kuriboh boys cheek, a weak cry came out "Jaden!" before the blue haired boy did some sort of face plant. The man hesitated for a moment to let a snort, as he watched the boy kick him away and jump backwards. It didn't really affect the man a lot, but at least he could see that the boy got some distance.

He noticed that he was panting badly but still had a slight crooked grin on his face, but his eyes were serious, trying to plan something, trying to find some way out of this predicament.

As if the heavens had answered the boys calls, a loud voice called out from a side building, a figure stood there, a cloak covering it's body, but an arm outside of the cloak with a duel disk on.

"I summon! Red Eyes Black Dragon!"

If he were to say, it was more of a battle cry than anything, but still he watched intently as the man about to punch the Kuriboh boy gasped, and stepped back a bit, clearly in shock and partly fear. He noticed how the Kuriboh boy seemed to let out a sigh of relief, it would of seemed that he didn't need to come up with a plan.

He watched in some what amazement as a black dragon swooped down from the roof that the cloaked man was on, and flew towards the man, preparing to attack. Attack he did, as the man let out a scream in agony, falling to his knee's when the dragon finally shot a red beam of light at him, before swooping back up in to the sky and letting out a battle roar before finally disappearing.

The figure then did something that he did not advise and jumped off the two story factory like building, landing in a slightly crouched pose seeming perfectly fine. But of course the jump was not perfect, it could be seen by the way the man stumbled and let out a curse under his breath before running over to the boys.

"Jaden! Syrus!" He yelled as he looked directly at the two boys, of course one wouldn't know because he was on the ground unconscious. He couldn't help but make a mental note about how he seemed to turn slightly in his direction then back over to the two boys.

"Jono-san!" The Kuriboh boy, who he assumed was named Jaden by the way that Jono seemed to turn slightly in each of their individual directions when he said their names.

"We haven't got much time, can you run?" The Jaden boy just nodded, before dusting himself off slightly a grinning. "Good, grab Syrus, we need to get going before others come."

"Excuse me, but would you care to explain what's going on?" He called out, getting the boy and the cloaked man's full attention.

"Ah... well...Eh... i can't really explain now, just trust us and follow us! It'll be bad if they get you." He said before quickly turning to look around carefully, he seemed a bit paranoid. He stood up brushing himself off, looking back at his other meant to be dead friends, as they also stood up, brushing themselves off while throwing confused looks about.

The Jono guy, who he swore that he recognized, seemed to beckon them over, while the Jaden boy picked up the Syrus boy and put him on his back before walking over. Being that he was confused he just followed - meaning that everyone followed him - hoping to get answers later.

'This is bad.' That was the only thought going through Joey's mind, as he carefully weaved his ways through alley ways, only going on to the main road or a path after he had looked around the gray leftovers of a once shining city. He had to be careful, all he needed to do was to get to Kaiba Co. and then they would be safe - ish.

Of course he wasn't going to the KC in the center of the city, that would be where 'they' were most active, so he had to go to another one, another hidden one, one that 'they' wouldn't be able to get to so easily.

His job was made harder, by having one unconscious blue haired boy on another injured brown haired boys back. Not to mention the Egyptian people, tagging along looking like they had just been sucked through a portal to another world in their sleep - which was technically true.

Either way, he had to do, what he had to do, or he wasn't Joey Wheeler the third ranked duelist in the world, and one of the commanders of the rebels, although what they did was good, even if it was a little shady - but that's what it would of been counted as when it was still the bright shining city of Domino.

He weaved around another corner, stopping for a moment and looking around as if he was being chased by a mad man - which again, was kinda true. He was about to make a break for it and sprint across the abandoned road, when he noticed one of 'their' evil little minions, a duel disk on one arm, a gun in the other. He was about to duck back when the guy spotted him, pointing his gun in his direction, he swallowed down nothing, all his gulping water had been spent on the sweat that was pouring about of his forehead.

He closed his eyes tightly as he saw the finger about to go down on to the trigger, when he suddenly heard a screech, he slowly opened his eyes and let out a light sigh and smiled cheesily.

His grin only grew when he saw the door to the van fly open in their direction. "Quickly in!" He heard a cry come from the van and he looked at the others and gestured towards the van before sprinting with all his might, sparing a glance for his could-of-been assassin, who was laying on the ground - not due to being hit by a car, but having his pressure point pushed on the back of his neck by one of the people who had kindly opened the door just in time.

He slammed the back of the van shut as soon as everyone was in, and ran round to the front doors which had been opened for him and launched himself at the seat, slamming the door behind and barely having enough time to put his seat belt on, before yelling "Drive!" at the slightly amused looking pointy haired brunet.

That point haired brunet, slammed his foot down on the pedal at that command, and drove off sliding through the roads as fast as he could, after all they were in a very big hurry.

A certain innocent - but now strong and powerful - looking, tri-coloured, star shaped hared boy gritted his teeth in annoyance, anticipation and anger as he stared up at the ceiling.

They were meant to be back by now, he had gotten Joey to go and help them out, since he feared the worst when the two young boys hadn't returned almost half an hour after they were meant to, he knew that sometimes things dragged out and that sometimes they were late, but they had never been this late in a time of need and worry.

He let out a sigh as he turned to a man sitting at a desk brunet hair covering the most part of his eyes as he typed away, at amazing speed, on a laptop, pausing every few moments, before looking up at him, then going back to his work.

"They can take care of themselves you know, after all, they did go to MY academy." The brunet mumbled aloud to the star haired boy.

"That may be so Kaiba, but they were at your academy when it was still considered 'safe' to go out on to the streets." He shot back to Kaiba, who just frown and let out a small growl from the back of his throat.

"You know, you should get your bangs cut." Came a rather unexpected response from the grumpy man typing away. "After all, we can barely see your eyes, keep it up and you'll turn in to a sheep dog, you'll look even more ridicules than you did before."

There was a pause of silence in the office, before two chuckles broke out filling in the silence. It was just like Kaiba to try to give them a break from the crushing atmosphere - well, it was in times like this, any other time and it would of been taken like a real insult and would of been followed by a very awkward silence and then someone trying to kill someone - namely Joey - but it was nice to have short breaks even if it came from the all serious Seto Kaiba.

Before they knew it the door flew open, leading entry to one dog boy, two younger boys, and some rather confused looking Egyptian people.

"Great, nothing smells worst than wet dog." Came a mumble from Seto, as he took one glance at the drenched from head to toe Wheeler, before going back to work.

"Why yo-" He was soon cut off quickly by seeing that the other person in the room has stood up to greet them. "Hey, Yug? worried about us?" He said loudly while walking up to Yugi, and putting him in a friendly - as friendly as it can get - head lock and ruffling some of his hair, before a rather sharp elbow collided with his ribs, and he let go and was holding his side in pain.

"You know i was worried about you, i would of gone myself, besides it wasn't really you i was worried about." The elbower said as he glanced towards the two boys who seemed to be barely standing, he quickly helped the injured boy by taking his load off and picking up Syrus.

"Relax, you had nothing to worry about, especially when Joey Wheeler's on the job" The now recovered Joey said point to himself with his thumbs.

"That was the reason he was worried." Came the voice of Kaiba who was still sitting and typing by the laptop, as Yugi put Syrus down on the sofa, giving him a quick look over before letting out a sigh, he distantly heard Joey yelling something about picking a fight with Kaiba, but dismissed it for the moment.

"Could you tell us what the hell is going on now?!" A rather annoyed Pharaoh snapped, he was confused and had reached near the end of his patience. Yugi's head snapped up and looked directly towards him before he sighed and sat down on the sofa.

"uhh... well..." Yugi said trying to word it, before someone else stepped in.

"A mad man has taken over the place, has messed up time and has done some sort of weird thing to practically 'enslave' or rather put the whole city under his control, because he's a money lusting idiot that doesn't know the first thing about taking over the world. Also some how he has made duel monsters real, but you still summon them with cards and we are what you could call the 'rebellion', although i think it's a stupid way to put it." Came a slightly high pitched voice, of a young Kaiba, who had just entered the room.

"Mokuba, your meant to be resting." Snapped the rather angry voice of the older Kaiba, who was now standing.

"But Seto-"

"No, you'll open your wounds if your up and about." Seto's hands were clenched tightly and looked like his finger nails could be digging in to his skin.

"Bu-"

"You should listen to your brother, Mokuba, your injured after all you were shot." Surprisingly enough that came from Joey, but it looked like that Yugi would open his mouth to say something is Mokuba didn't go back then. Not many people also missed the way that Seto stiffened slightly when the word 'shot' came up in the same sentence as his brother's name.

"Fine, but as soon as it's better I'm going to be up and about and your not stopping me!" He said stubbornly as he walked out of the room almost stomping his feet all the way.

Silence rang through out the room, no one really knew that to do, but Kaiba finally sat down and let out a sigh before finally going back to his work, but he seemed a bit more rigidly than normal. Yugi tipped his head back and stared up at the ceiling thinking everything through, he bit his lip trying to see how it came to this, he remembered quite well, but what he remembered wasn't the main trigger, it was just a part of a chain that made his life just a bit harder.

"Anyone care to put it in more detail?" Said someone other than the pharaoh, no this came from a moment with long black hair and wisdom shining in her eyes.

"That's just it, most of the stuff that had happened, was already done before we even knew about it, it was amazing how well they avoided our radar. Although the reason why most of us are on the run, is because we openly refused to join a criminal organization, in front of the whole world. Let's just say, they weren't to happy, so it's either we are found and forced to join or we are killed dead on the spot, but considering the people here they wouldn't kill us, they'd more likely end up capturing us - after all, Criminal activities aren't really our style." Said Yugi, as he sank further in to the sofa, sighing as he kept thinking things through.

"Who is this mad man?" The Pharaoh questioned carefully, his eyes scanned over Yugi, it was clear that he was tired, worried and most likely uneasy - maybe even scared, but even if he was he knew that Yugi wasn't the kind to shake in his boots.

"There are many, but the main one goes by the name of - Zorc."

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**A/N: That's it for the prologue, I would like to know what people think about this story and if there is any interest in continuing. I will warn you that I am not a frequent updater as of late, and my writing style has severally changed. I do not think this chapter has even been beta read, but I think I have skimmed through it a few times. If this story were to continue I think I will have to go out and find a Beta reader, if I don't have one I normally don't update at all :/ - If this story were to continue I will remind you that the style may drastically differ from what is written in this chapter, I wrote this around the time I first started liking Yu-Gi-Oh, and that's quite a while back (a year or so), so my writing style has changed - whether it has improved I'm not sure. But this chapter may be a little too childish and may end up being rewritten if it really is the case.**

**Thank you for reading, I would greatly appreciate any constructive reviews or just telling me if you think this story would be interesting enough to continue. Thank you :). **


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